BioMCP

# CLI Reference BioMCP provides one command family with entity-oriented subcommands. ## Global options - `--json`: return structured JSON output - `--no-cache`: bypass HTTP cache for the current command ## Core command patterns ```text biomcp search <entity> [filters] biomcp get <entity> <id> [section...] ``` Section names are positional trailing arguments after `<id>`. ## Top-level commands ```text biomcp search ... biomcp get ... biomcp enrich <GENE1,GENE2,...> [--limit N] biomcp batch <entity> <id1,id2,...> [--sections ...] [--source ...] biomcp health [--apis-only] biomcp list [entity] biomcp skill [list|install|<name>] biomcp mcp biomcp serve biomcp serve-http [--host 127.0.0.1] [--port 8080] biomcp update [--check] biomcp uninstall biomcp version ``` ## Search command families ### Gene ```bash biomcp search gene -q BRAF --limit 10 --offset 0 ``` ### Disease ```bash biomcp search disease -q melanoma --source mondo --limit 10 --offset 0 ``` ### PGx ```bash biomcp search pgx -g CYP2D6 --limit 10 biomcp search pgx -d warfarin --limit 10 ``` ### Phenotype (Monarch semsim) ```bash biomcp search phenotype "HP:0001250 HP:0001263" --limit 10 ``` ### GWAS ```bash biomcp search gwas -g TCF7L2 --limit 10 biomcp search gwas --trait "type 2 diabetes" --limit 10 ``` ### Article ```bash biomcp search article -g BRAF -d melanoma --since 2024-01-01 --limit 5 --offset 0 ``` ### Trial ```bash biomcp search trial -c melanoma --status recruiting --source ctgov --limit 5 --offset 0 ``` ### Variant ```bash biomcp search variant -g BRAF --hgvsp V600E --limit 5 --offset 0 ``` ### Drug ```bash biomcp search drug -q "kinase inhibitor" --limit 5 --offset 0 ``` ### Pathway ```bash biomcp search pathway -q "MAPK signaling" --limit 5 --offset 0 ``` ### Protein ```bash biomcp search protein -q kinase --limit 5 --offset 0 biomcp search protein -q kinase --all-species --limit 5 ``` ### Adverse event ```bash biomcp search adverse-event --drug pembrolizumab --serious --limit 5 --offset 0 biomcp search adverse-event --type device --manufacturer Medtronic --limit 5 biomcp search adverse-event --type device --product-code PQP --limit 5 ``` ## Get command families ### Gene ```bash biomcp get gene BRAF biomcp get gene BRAF pathways biomcp get gene BRAF diseases ``` ### Disease ```bash biomcp get disease melanoma biomcp get disease MONDO:0005105 genes phenotypes biomcp get disease MONDO:0005105 variants models biomcp get disease MONDO:0005105 pathways prevalence civic biomcp get disease MONDO:0005105 all ``` ### PGx ```bash biomcp get pgx CYP2D6 biomcp get pgx codeine recommendations frequencies biomcp get pgx warfarin annotations ``` ### Article ```bash biomcp get article 22663011 biomcp get article 22663011 fulltext ``` ### Trial ```bash biomcp get trial NCT02576665 biomcp get trial NCT02576665 eligibility ``` ### Variant ```bash biomcp get variant "BRAF V600E" biomcp get variant "BRAF V600E" predict biomcp get variant rs7903146 gwas ``` ### Drug ```bash biomcp get drug pembrolizumab biomcp get drug carboplatin shortage ``` ### Pathway ```bash biomcp get pathway R-HSA-5673001 biomcp get pathway R-HSA-5673001 genes ``` ### Protein ```bash biomcp get protein P15056 biomcp get protein P15056 domains interactions ``` ### Adverse event ```bash biomcp get adverse-event 10222779 biomcp get adverse-event 10222779 reactions outcomes biomcp get adverse-event 10222779 concomitant guidance all ``` ## Enrichment ```bash biomcp enrich BRAF,KRAS,NRAS --limit 10 biomcp enrich BRAF,KRAS,NRAS --limit 10 --json ``` ## MCP mode - `biomcp serve` runs the stdio MCP server. - `biomcp serve-http` runs MCP over HTTP/SSE. See also: `docs/reference/mcp-server.md`. ## Helper command families ```bash biomcp variant trials "BRAF V600E" biomcp variant articles "BRAF V600E" biomcp variant oncokb "BRAF V600E" biomcp drug adverse-events pembrolizumab biomcp drug trials pembrolizumab biomcp disease trials melanoma biomcp disease drugs melanoma biomcp disease articles "Lynch syndrome" biomcp gene trials BRAF biomcp gene drugs BRAF biomcp gene articles BRCA1 biomcp gene pathways BRAF biomcp pathway drugs R-HSA-5673001 biomcp pathway articles R-HSA-5673001 biomcp pathway trials R-HSA-5673001 biomcp protein structures P15056 biomcp article entities 22663011 ``` ## Batch mode ```bash biomcp batch gene BRAF,TP53 biomcp batch gene BRAF,TP53 --sections pathways,interactions biomcp batch trial NCT02576665,NCT03715933 --source nci biomcp batch variant "BRAF V600E","KRAS G12D" --json ```